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Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19980715)19:9<1001::aid-jcc2>3.0.co;2-uopenalex-snapshot
Directional hydrogen bonding in the MM3 force field: II
inferredcites →https://doi.org/10.1002/1096-987x(200103)22:4<418::aid-jcc1012>3.0.co;2-3openalex-snapshot
Effect of ligand volume correction on PMF scoring
inferredcites →https://doi.org/10.1002/jcc.21378openalex-snapshot
New angle‐dependent potential energy function for backbone–backbone hydrogen bond in protein–protein interactions
inferredcites →https://doi.org/10.1002/jcc.540111014openalex-snapshot
The nature of the N H…OC hydrogen bond: An intermolecular perturbation theory study of the formamide/formaldehyde complex
inferredcites →https://doi.org/10.1002/poc.610071103openalex-snapshot
Directional hydrogen bonding in the MM3 force field. I
inferredcites →https://doi.org/10.1002/prot.10567openalex-snapshot
NH…O, OH…O, and CH…O hydrogen bonds in protein–ligand complexes: Strong and weak interactions in molecular recognition
inferredcites →https://doi.org/10.1006/jmbi.1994.1334openalex-snapshot
Satisfying Hydrogen Bonding Potential in Proteins
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
inferredcites →https://doi.org/10.1016/s0022-2836(03)00021-4openalex-snapshot
An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
inferredcites →https://doi.org/10.1016/s0959-440x(00)00195-0openalex-snapshot
Statistical potentials and scoring functions applied to protein–ligand binding
inferredcites →https://doi.org/10.1016/s1359-6446(02)02478-9openalex-snapshot
Application of hydrogen bonding calculations in property based drug design
inferredcites →https://doi.org/10.1021/ar010054topenalex-snapshot
Hydrogen Bridges in Crystal Engineering: Interactions without Borders
inferredcites →https://doi.org/10.1021/ci100182copenalex-snapshot
Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions
inferredcites →https://doi.org/10.1021/ci100343jopenalex-snapshot
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?
inferredcites →https://doi.org/10.1021/ci7004719openalex-snapshot
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA
inferredcites →https://doi.org/10.1021/cr800346fopenalex-snapshot
What Is the Covalency of Hydrogen Bonding?
inferredcites →https://doi.org/10.1021/ct800267xopenalex-snapshot
Geometrical Preferences of the Hydrogen Bonds on Protein−Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations
inferredcites →https://doi.org/10.1021/ct9005695openalex-snapshot
Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins
inferredcites →https://doi.org/10.1021/j100011a013openalex-snapshot
A Simple Functional Representation of Angular-Dependent Hydrogen-Bonded Systems. 1. Amide, Carboxylic Acid, and Amide-Carboxylic Acid Pairs
inferredcites →https://doi.org/10.1021/ja0319994openalex-snapshot
An Empirical Backbone−Backbone Hydrogen-Bonding Potential in Proteins and Its Applications to NMR Structure Refinement and Validation
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot
DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
inferredcites →https://doi.org/10.1021/jm100112jopenalex-snapshot
A Medicinal Chemist’s Guide to Molecular Interactions
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/jp000644topenalex-snapshot
Development of a Knowledge-Based Potential for Crystals of Small Organic Molecules: Calculation of Energy Surfaces for C=0···H−N Hydrogen Bonds
inferredcites →https://doi.org/10.1021/jp011042sopenalex-snapshot
Hydrogen Bond Energetics: A Simulation and Statistical Analysis of N-Methyl Acetamide (NMA), Water, and Human Lysozyme
inferredcites →https://doi.org/10.1023/a:1007999920146openalex-snapshot
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
inferredcites →https://doi.org/10.1073/pnas.0307578101openalex-snapshot
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
inferredcites →https://doi.org/10.1093/nar/gkh785openalex-snapshot
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys
inferredcites →https://doi.org/10.1186/1471-2105-11-128openalex-snapshot
New statistical potential for quality assessment of protein models and a survey of energy functions
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/jcc.23170openalex-snapshot
Water PMF for predicting the properties of water molecules in protein binding site
inferred← citeshttps://doi.org/10.1002/jmr.2266openalex-snapshot
Latest developments in molecular docking: 2010–2011 in review
inferred← citeshttps://doi.org/10.1007/s00894-013-2005-7openalex-snapshot
A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions
inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.008openalex-snapshot
Can docking scoring functions guarantee success in virtual screening?
inferred← citeshttps://doi.org/10.1016/bs.pmch.2021.01.004openalex-snapshot
Use of molecular docking computational tools in drug discovery
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107884openalex-snapshot
Finding the direct energy-structure correlations in intramolecular aromaticity assisted hydrogen bonding (AAHB)
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00560openalex-snapshot
Computer Modeling of Halogen Bonds and Other σ-Hole Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01961openalex-snapshot
Enhancing Generalizability in Protein–Ligand Binding Affinity Prediction with Multimodal Contrastive Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02505openalex-snapshot
ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00677openalex-snapshot
TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00179openalex-snapshot
Hydroxyl Groups in Synthetic and Natural-Product-Derived Therapeutics: A Perspective on a Common Functional Group
inferred← citeshttps://doi.org/10.1021/acsmeasuresciau.6c00076openalex-snapshot
β-Anomeric Mannopentaose-Based Nonenzymatic NIR Glucose Sensor Enabling Cost-Effective Continuous Monitoring
inferred← citeshttps://doi.org/10.1021/ci3002638openalex-snapshot
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
inferred← citeshttps://doi.org/10.1021/ci500647fopenalex-snapshot
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy
inferred← citeshttps://doi.org/10.1021/ci500731aopenalex-snapshot
Classification of Current Scoring Functions
inferred← citeshttps://doi.org/10.1039/c5sc00534eopenalex-snapshot
Virtual screening for high affinity guests for synthetic supramolecular receptors
inferred← citeshttps://doi.org/10.1515/cmb-2019-0009openalex-snapshot
CBSF: A New Empirical Scoring Function for Docking Parameterized by Weights of Neural Network
inferred← citeshttps://doi.org/10.4155/fmc-2016-0143openalex-snapshot
Molecular Docking for Drug Discovery and Development: A Widely Used Approach but Far from Perfect
inferred← citeshttps://doi.org/10.70675/2b288725z2446z48c5z833ezf53915cd324bopenalex-snapshot
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